carma molecular dynamics

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What is Carma ?

Carma is a stand-alone molecular dynamics analysis tool tuned for the DCD-PSF world. The program is free, open-source software and is immediately available for download via this page. Carma can calculate the variance-covariance and cross-correlation matrices, do a principal component analysis using both Cartesian PCA and dihedral angle PCA, do a PCA-based cluster analysis, remove overall rotations/translations, calculate the mass-weighted radius of gyration, calculate the average CA-CA distance map and the rmsd from it (for the length of the trajectory), calculate the average structure and atomic rms fluctuations, calculate distances and torsion angles between arbitrary sets of atoms, calculate solute's entropy using both Schlitter's and Andricioaei's formulas, allow a primitive quick view of a trajectory on a X11-capable terminal, calculate CNS- and XPLOR-compatible density maps representing the average distribution of selected atomic species (eg. ions or waters), etc.

What is this group for ?

The aim of this google group is to provide a forum for sharing announcements, bug reports and implementation details for the program. This is a tightly moderated and extremely low volume group that will not disturb your peace of mind. To avoid spammers spamming us to death, the very first message of any member will be moderated.

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Placido Rojas Franco, Nicholas M. Glykos2

Mar 24

Install Carma Widnows

> Hello, How can I Install Carma In Windows? for analysis H-bond, RMS and > Radious gyrus The

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Install Carma Widnows

> Hello, How can I Install Carma In Windows? for analysis H-bond, RMS and > Radious gyrus The

Mar 24

chet...@gmail.com, Nicholas Glykos2

Mar 20

dPCA analysis ends in error "Error in LAPACK ssyev() call: 663"

Maximum of variance-covariance matrix is -999999995904.000000 Minimum of variance-covariance matrix

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dPCA analysis ends in error "Error in LAPACK ssyev() call: 663"

Maximum of variance-covariance matrix is -999999995904.000000 Minimum of variance-covariance matrix

Mar 20

YED, Nicholas M. Glykos5

12/27/23

Thank you very much. I used the correct task in grcarma and it worked. I hope you have a great day.

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Thank you very much. I used the correct task in grcarma and it worked. I hope you have a great day.

12/27/23

Mandira Dinda, Nicholas M. Glykos2

11/7/23

Entropy calculation as a function of time

> Is it possible ti calculate entropy as a function of time?From > earlier discussion what I

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Entropy calculation as a function of time

> Is it possible ti calculate entropy as a function of time?From > earlier discussion what I

11/7/23

Mandira Dinda, Nicholas M. Glykos5

10/12/23

Unable to eliminate overall Translational and rotational Motion

I have successfully calculated the entropy of my system using PSF file generated by CHARMM-GUI by

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Unable to eliminate overall Translational and rotational Motion

I have successfully calculated the entropy of my system using PSF file generated by CHARMM-GUI by

10/12/23

Nicholas M. Glykos

10/10/23

Re: Unable to calculate the entropy values in schlitter's of a protein system

You are trying to calculate the entropy of not just the solute (protein), but of the whole system (

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Re: Unable to calculate the entropy values in schlitter's of a protein system

You are trying to calculate the entropy of not just the solute (protein), but of the whole system (

10/10/23

8/2/23

Job opening in VMD (Visual Molecular Dynamics) development Team

Hi Folks, We have an amazing opportunity for those interested in working closely with the VMD

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Job opening in VMD (Visual Molecular Dynamics) development Team

Hi Folks, We have an amazing opportunity for those interested in working closely with the VMD

8/2/23

Nicholas M. Glykos

5/7/23

carma v.2.3 released.

Dear All, A new stable version (v.2.3) of carma & friends has been released and is available for

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carma v.2.3 released.

Dear All, A new stable version (v.2.3) of carma & friends has been released and is available for

5/7/23

Nicholas M. Glykos

4/12/23

Clustering of molecular dynamics structures : new program available for testing.

Dear All, We have developed a new program for clustering structures from a trajectory using the data

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Clustering of molecular dynamics structures : new program available for testing.

Dear All, We have developed a new program for clustering structures from a trajectory using the data

4/12/23

Gagan Jyot, Nicholas Glykos2

2/21/23

Sorry for the delay, gmail decided to send the mail to the spam folder. If you still have the issue,

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Sorry for the delay, gmail decided to send the mail to the spam folder. If you still have the issue,

2/21/23

Gagan Jyot, Nicholas Glykos6

1/16/23

How to change no. of frames

I do not have practical experience from the analysis you are doing. I would try to locate at which of

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How to change no. of frames

I do not have practical experience from the analysis you are doing. I would try to locate at which of

1/16/23

Jessica M. Gonzalez-Delgado, Nicholas M. Glykos13

3/18/22

Calculating overall protein tumbling time

Yup, that did it! Now carma is running. I'll try it on a longer trajectory, but it should work as

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Calculating overall protein tumbling time

Yup, that did it! Now carma is running. I'll try it on a longer trajectory, but it should work as

3/18/22

Nicholas M. Glykos

8/25/21

Re: The unit J/molK transform in Carma

It is J mol⁻¹ K⁻¹ On Wed, Aug 25, 2021 at 06:12:13PM +0800, Qifeng Bai wrote: > Dear Nicholas

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Re: The unit J/molK transform in Carma

It is J mol⁻¹ K⁻¹ On Wed, Aug 25, 2021 at 06:12:13PM +0800, Qifeng Bai wrote: > Dear Nicholas

8/25/21

venkat, … Diana A. Valencia6

6/4/21

Water ions removing step getting error -reg

I would like to comment that in my cause the protein was segment 'U' (I don't know why)

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Water ions removing step getting error -reg

I would like to comment that in my cause the protein was segment 'U' (I don't know why)

6/4/21

Lilian Esmeralda Araujo Arcos, Nicholas Glykos2

10/26/20

Please see from the documentation (https://utopia.duth.gr/glykos/pdf/carma.pdf) pages 1 & 2. On

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Please see from the documentation (https://utopia.duth.gr/glykos/pdf/carma.pdf) pages 1 & 2. On

10/26/20

Jessica Gonzalez Delgado, Nicholas M. Glykos2

8/11/20

backbone N-H trajectory analysis

> I'm new to MD simulations. I'm wondering how to do a trajectory analysis > for

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backbone N-H trajectory analysis

> I'm new to MD simulations. I'm wondering how to do a trajectory analysis > for

8/11/20

suji george, Nicholas M. Glykos2

7/29/20

SEEING’ THE MOTION CORRESPONDING TO A SELECTED PRINCIPAL COM- PONENT in dpca

> Is there a way to see the motion corresponding to a selected priniciple > component in

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SEEING’ THE MOTION CORRESPONDING TO A SELECTED PRINCIPAL COM- PONENT in dpca

> Is there a way to see the motion corresponding to a selected priniciple > component in

7/29/20

jose correa, Nicholas M. Glykos2

6/19/20

Unidentified keyword or argument : −v. Abort.

> carma −v −w −fit −atmid ALLID −segid A hsa-i-5d.dcd hsa-wi.psf > > Unidentified keyword or

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Unidentified keyword or argument : −v. Abort.

> carma −v −w −fit −atmid ALLID −segid A hsa-i-5d.dcd hsa-wi.psf > > Unidentified keyword or

6/19/20

Manori Jayasinghe, Nicholas M. Glykos2

5/22/20

Varience-Covarience matrix and normalized cross-correlation matrix

> I used the Carma package to compute the Varience-covarience matrix and the > normalized cross

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Varience-Covarience matrix and normalized cross-correlation matrix

> I used the Carma package to compute the Varience-covarience matrix and the > normalized cross

5/22/20

Nicholas M. Glykos

2/6/20

Carma v.2.01 released.

Dear All, A new stable version of carma v.2.01 has been released. This release adds support for 64bit

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Carma v.2.01 released.

Dear All, A new stable version of carma v.2.01 has been released. This release adds support for 64bit

2/6/20

Nicholas M. Glykos

12/29/19

Illustrating transitions between conformers using circos plots

Dear All, If you want to illustrate transitions between different conformations (identified from

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Illustrating transitions between conformers using circos plots

Dear All, If you want to illustrate transitions between different conformations (identified from

12/29/19

Ruikang Yuan, … Nicholas M. Glykos13

11/12/19

Something went wrong. For details check last_carma_run.log located in

I install xterm in my ubuntu. And I input xterm in my gnome-terminal then another terminal opens. I

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Something went wrong. For details check last_carma_run.log located in

I install xterm in my ubuntu. And I input xterm in my gnome-terminal then another terminal opens. I

11/12/19

Nicholas M. Glykos

8/13/19

> In figure 4.a of attached paper, how could I have the plot of the proportion > of variance

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> In figure 4.a of attached paper, how could I have the plot of the proportion > of variance

8/13/19

Nicholas M. Glykos

8/11/19

> 1) Is carma clustering method base on RMSD? https://arxiv.org/abs/1512.04024 > 2) after

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> 1) Is carma clustering method base on RMSD? https://arxiv.org/abs/1512.04024 > 2) after

8/11/19

Nicholas M. Glykos2

8/10/19

Re: A problem about clustering

Please do keep the carma mailing list in the CC of the messages (see the header of this message), so

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Re: A problem about clustering

Please do keep the carma mailing list in the CC of the messages (see the header of this message), so

8/10/19

amit, Nicholas M. Glykos6

6/26/19

plotting of cPCA.3d_landscape

> I am not able to create the same image sent by you. can u send me > screenshot (vmd)

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plotting of cPCA.3d_landscape

> I am not able to create the same image sent by you. can u send me > screenshot (vmd)

6/26/19

Adeniyi Olajide, nmgl...@gmail.com2

4/26/19

carma software download

On Friday, April 26, 2019 at 11:45:00 PM UTC+3, Adeniyi Olajide wrote: Hi, I am having issues

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carma software download

On Friday, April 26, 2019 at 11:45:00 PM UTC+3, Adeniyi Olajide wrote: Hi, I am having issues

4/26/19

Nicholas M. Glykos

4/18/19

Re: preparation of amber topology file in carma

> I am Aashish Bhatt form INST-Mohali(India). Sir in my system we used amber > topology file

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Re: preparation of amber topology file in carma

> I am Aashish Bhatt form INST-Mohali(India). Sir in my system we used amber > topology file

4/18/19

Fulbabu, Nicholas M. Glykos10

2/12/19

dPCA not running

> I have the plot but how do I get the color bar (CB) for the plot? If you want to prepare plots

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dPCA not running

> I have the plot but how do I get the color bar (CB) for the plot? If you want to prepare plots

2/12/19

Fulbabu, Nicholas M. Glykos5

2/9/19

Convert Amber.prmtop to .psf for Carma input

Got it. *************** Kind regards Md Fulbabu Sk Ph.D. Research Scholar Discipline of BioSciences

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Convert Amber.prmtop to .psf for Carma input

Got it. *************** Kind regards Md Fulbabu Sk Ph.D. Research Scholar Discipline of BioSciences

2/9/19

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